I understand the margins of error, but sometimes, the cover is just wayyy off (meaning 1/8 inch | 3mm or more). However, Amazon will randomly put pages from other books, have parts upside down, etc. Printing the right book (a lot of authors like to go live vs proofs to get reviews in early and have proofs count as sales, then market after everything feels good). The things I've had the hardest time with in some of their most recent changes are: That should be all you need, but is there a reason you used pixels for the PDF instead of millimeters or inches? Amazon KDP has templates it will create for you based on your page count to get exact dimensions for everything. That will ensure it flattens everything in your document properly and leaves no weird issues with layers sticking out. I used to use press-ready before the post above. PDF x-1a:2003 is definitely the way to go for print files. They require your print file (assuming you have one as well based on photo and export settings) to be CMYK color space if you do have hard copies.

I just looked at several random inside looks, even from top books, and yes, they are garbage in quality on the initial look inside load. I've noticed that it, along with the thumbnails on a book's page, take a few seconds to buffer. As long as your actual thumbnails, eBook, and print are fine, you kind of have to go with what they give you for preview-related content. They might even lower the quality on purpose to keep theft down, help with bandwidth, etc. Those must be in an RGB color space to upload. All of the ones I design for come out great digitally at the size mentioned above.

Your post says the Kindle version is fine, as is expected (they like thumbnails around 1600x2560 pixels), but I'm not sure if you meant on a Kindle it is fine, but on Amazon's site, the Thumbnail is bad. Way fewer issues arise with colors that are not very dark (or red skin due to the human tone map), but I have a few questions to help out. Those are more suited to cover design than Photo, and I find Publisher is most ideal for Photo-based covers (it also has a Photo persona for similar controls). That article linked to above was my question, partially related to how Publisher vs Designer (more issues for me) seems to get along with Amazon and their newer 3rd party printing companies. I've had all sorts of go arounds with Amazon via Affinity files.

Affinity photo workbook amazon